Summary The elicitation of effective affinity maturation has proven to be an essential component of efficacious humoral vaccines. In fact, recent findings in vaccine development for influenza and HIV-1 suggest that success in these key areas may depend on the ability to enhance affinity maturation to an extent not yet possible. It is the overarching goal of this U19 research project to use highly focused mathematical modeling driven by state-of-the art experimentation to advance our understanding of the interconnected complex processes that together constitute affinity maturation in the humoral response to vaccine immunogens. In this project, we will develop and fit key components of the affinity maturation model including the generation of antibody diversity through somatic hypermutation and the correspondence between antibody amino acid sequence and affinity of the antibody and the eliciting antigen. Somatic hypermutation modeling will be driven by experiments in passenger-transgene engineered mice, which express a single productive antibody gene and contain an identical but transcription-disabled gene on the other chromosome, which mutates without experiencing selection. Affinity modeling will be driven by data generated in project 2 (high-throughput sequence and affinity in a murine system) and project 3 (structure and affinity studies) and pursued using a combination of biophysical and statistical modeling. We have designed and will carry out a study of affinity maturation in the response of human vaccinees to influenza vaccine in two successive years. Sequence and affinity data from these studies will be used to identify antibodies and antibody clones to be studied in detail in the mouse transgene system and in the structural studies. The inter- and intra-clonal dynamics obtained in these studies will in turn be analyzed using the models developed. The research team from this project will participate in statistical data analysis throughout the overall program. The software and methods developed under this program will be made available to the broader research community, and relevant training made available to ensure their effective use. These resources, together with the insights into the mechanics of diversification and selection under affinity maturation that will be forthcoming from our research efforts, promise to bring substantial opportunities for the development of novel approaches in vaccinology.